LOL -- that's "shorting agains the box" and there is no such thing as making money "shorting against the box" because it's a net neutral position. It used to be a way to temporarily "sell" without owing taxes or "sell" to lock in a gain on restricted shares, but it's impossible to claim a profit from it lol
If you "made" $50K shorting your own shares on JBII then you also lost $50k at the exact same time on your long side. Your broker probably just sold your own shares (actually that's exactly what he did) and then told you "sure, okay, you have both a long and a short....enjoy yourself lol" then charged you double commission.